Well, I really don't have the same problem you do, Nyeshet. My house rule for multiclassing is that each class beyond the first gives you the -20% XP penalty, period. Favored class becomes a much bigger factor (you still ignore it for purposes of determining your XP penalty) and it promotes multi-class characters of non-human races to take levels in their favored class as opposed to something else. Also, each prestige class beyond the first gives you a -20% xp penalty.
Personally, my problem with the multi-classing rules is that it is simply too easy and often too beneficial to multiclass (especially if you are a fighter). You are a rogue and take one level of fighter to get some more hit points and a bonus feat to help you in combat, plus you are proficient with all armor, shields, and weapons now. YAY! Or the fighter who decides to become a wizard and just immediately learns all the stuff a 1st level wizard took years, often decades, to master. Plus, you can cast shield and true strike now, all for the cost of a few hp (who will miss really miss them often enough to care) and one BAB. Besides, you've upped your will save which never hurts.
Dipping into classes just to snag a few useful abilities is all too common in 3e. All it leads to is mutts who are neither realistic, nor well-defined character types. It is more acceptable in high-fantasy/high-power worlds like FR, but in most places it really sucks.